ks-package: ks

Description Details Author(s) References See Also


Kernel smoothing for data from 1- to 6-dimensions.


There are three main types of functions in this package:

The kernel used throughout is the normal (Gaussian) kernel K. For 1-d data, the bandwidth h is the standard deviation of the normal kernel, whereas for multivariate data, the bandwidth matrix H is the variance matrix.

–For kernel density estimation, kde computes

hat(f)(x) = n^(-1) sum_i K_H (x - X_i).

The bandwidth matrix H is a matrix of smoothing parameters and its choice is crucial for the performance of kernel estimators. For display, its plot method calls plot.kde.

–For kernel density estimation, there are several varieties of bandwidth selectors

–For kernel density derivative estimation, the main function is kdde

hat(f)^(r)(x) = n^(-1) sum_i D^r K_H (x - X_i).

The bandwidth selectors are a modified subset of those for kde, i.e. Hlscv, Hns, Hpi, Hscv with deriv.order>0. Its plot method is plot.kdde for plotting each partial derivative singly.

–For kernel discriminant analysis, the main function is kda which computes density estimates for each the groups in the training data, and the discriminant surface. Its plot method is plot.kda. The wrapper function hkda, Hkda computes bandwidths for each group in the training data for kde, e.g. hpi, Hpi.

–For kernel functional estimation, the main function is kfe which computes the r-th order integrated density functional

hat(psi)_r = n^(-2) sum_i sum_j D^r K_H (X_i - X_j).

The plug-in selectors are hpi.kfe (1-d), Hpi.kfe (2- to 6-d). Kernel functional estimates are usually not required to computed directly by the user, but only within other functions in the package.

–For kernel-based 2-sample testing, the main function is kde.test which computes the integrated L2 distance between the two density estimates as the test statistic, comprising a linear combination of 0-th order kernel functional estimates:

hat(T) = hat(psi)_0,1 + hat(psi)_0,2 - (hat(psi)_0,12 + hat(psi)_0,21),

and the corresponding p-value. The psi are zero order kernel functional estimates with the subscripts indicating that 1 = sample 1 only, 2 = sample 2 only, and 12, 21 = samples 1 and 2. The bandwidth selectors are hpi.kfe, Hpi.kfe with deriv.order=0.

–For kernel-based local 2-sample testing, the main function is kde.local.test which computes the squared distance between the two density estimates as the test statistic

hat(U)(x) = [hat(f)_1(x) - hat(f)_2(x)]^2

and the corresponding local p-values. The bandwidth selectors are those used with kde, e.g. hpi, Hpi.

–For kernel cumulative distribution function estimation, the main function is kcde

hat(F)(x) = n^(-1) sum_i intK_H (x - X_i)

where intK is the integrated kernel. The bandwidth selectors are hpi.kcde, Hpi.kcde. Its plot method is plot.kcde. There exist analogous functions for the survival function hat(bar(F)).

–For kernel estimation of a ROC (receiver operating characteristic) curve to compare two samples from hat(F)_1, hat(F)_2, the main function is kroc

(hat(F)_hat(Y1))(z), hat(F_hat(Y2))(z))

based on the cumulative distribution functions of hat(Yj)=hat(bar(F))_1(X_j), j=1,2.

The bandwidth selectors are those used with kcde, e.g. hpi.kcde, Hpi.kcde for hat(F)_hat(Yj), hat(bar(F))_1. Its plot method is plot.kroc.

–For kernel estimation of a copula, the main function is kcopula

hat(C)(z) = hat(F)(hat(F)_1^(-1)(z_1),..., hat(F)_d^(-1)(z_d))

where hat(F)_j^(-1)(z_j) is the z_j-th quantile of of the j-th marginal distribution hat(F_j). The bandwidth selectors are those used with kcde for hat(F), hat(F)_j. Its plot method is plot.kcde.

–For kernel mean shift clustering, the main function is kms. The mean shift recurrence relation of the candidate point x

x_j+1 = x_j + H D hat(f)(x_j)/hat(f)(x_j),

where j>=0 and x_0 = x, is iterated until x converges to its local mode in the density estimate hat(f) by following the density gradient ascent paths. This mode determines the cluster label for x. The bandwidth selectors are those used with kdde(,deriv.order=1).

– For kernel feature significance, the main function kfs. The hypothesis test at a point x is H0(x): H f(x) < 0, i.e. the density Hessian matrix H f(x) is negative definite. The test statistic is

W(x) = ||S(x)^(-1/2) vech H hat{f}(x)||^2

where H hat{f} is the Hessian estimate, vech is the vector-half operator, and S is an estimate of the null variance. W(x) is approximately chi-squared distributed with d(d+1)/2 degrees of freedom. If H0(x) is rejected, then x belongs to a significant modal region. The bandwidth selectors are those used with kdde(,deriv.order=2). Its plot method is plot.kfs.

–Binned kernel estimation is an approximation to the exact kernel estimation and is available for d=1, 2, 3, 4. This makes kernel estimators feasible for large samples.

–For an overview of this package with 2-d density estimation, see vignette("kde").


Tarn Duong for most of the package. M.P. Wand for the binned estimation, univariate plug-in selector and univariate density derivative estimator code. J. E. Chacon for the unconstrained pilot functional estimation and fast implementation of derivative-based estimation code. A. and J. Gramacki for the binned estimation for unconstrained bandwidth matrices.


Bowman, A. & Azzalini, A. (1997) Applied Smoothing Techniques for Data Analysis. Oxford University Press, Oxford.

Duong, T. (2004) Bandwidth Matrices for Multivariate Kernel Density Estimation. Ph.D. Thesis, University of Western Australia.

Scott, D.W. (1992) Multivariate Density Estimation: Theory, Practice, and Visualization. John Wiley & Sons, New York.

Silverman, B. (1986) Density Estimation for Statistics and Data Analysis. Chapman & Hall/CRC, London.

Simonoff, J. S. (1996) Smoothing Methods in Statistics. Springer-Verlag, New York.

Wand, M.P. & Jones, M.C. (1995) Kernel Smoothing. Chapman & Hall/CRC, London.

See Also

feature, sm, KernSmooth

ks documentation built on July 4, 2017, 9:45 a.m.

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